ciftify_recon_all --resample-to-T1w32k on completed ciftify output will not run

[asentis]

This may be user error, but I am unable to get the resample step to run on my existing ciftify_recon_all output. I am using the following command: ciftify_recon_all --resample-to-T1w32k --ciftify-work-dir /path/to/working_dir --fs-subjects-dir /path/to/working_dir/freesurfer Subj01

This is the error I receive: Subject output /path/to/working_dir/Subj01 already exists.If you wish to re-run, you must first delete old outputs.

Should I be using the --resample-to-T1w32k flag differently?

[edickie]

Thanks for letting me know. Which version of ciftify are you using? (that functionality will work for ciftify version 2.1.0 or later (or docker container fmriprep_ciftify:1.1.2-2.1.0 or later)..

[asentis]

Thanks for the quick response! I see, I'm running version 2.0.3. I just tried "pip install ciftify" and received "Requirement already satisfied.." notices. What is the best way to update to version 2.1.0 or the newest version?

[edickie]

Try

pip install --upgrade ciftify

On Wed., Sep. 11, 2019, 21:33 asentis, notifications@github.com wrote:

Thanks for the quick response! I see, I'm running version 2.0.3. I just tried "pip install ciftify" and received "Requirement already satisfied.." notices. What is the best way to update to version 2.1.0 or the newest version?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/edickie/ciftify/issues/123?email_source=notifications&email_token=ADEXT5VBUQPZPQFEDLCLEX3QJGL55A5CNFSM4IVYMLRKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6QL2SQ#issuecomment-530627914, or mute the thread https://github.com/notifications/unsubscribe-auth/ADEXT5TMWBVI3LHKERONN4DQJGL55ANCNFSM4IVYMLRA .

[asentis]

The resample flag worked perfectly with the upgraded version. Thank you!